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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ), 'gf_id' => 'HOM05D001356', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001356' ), 'data_identifier' => 'HOM05D001356', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001356', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '462', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p12580' => 'bna', 'A03p16520' => 'bna', 'A03p25330' => 'bna', 'A05p05670' => 'bna', 'A07p18830' => 'bna', 'A08p28180' => 'bna', 'A09p23850' => 'bna', 'A10p00210' => 'bna', 'Aa31LG1G11180' => 'aar', 'Aa31LG3G7400' => 'aar', 'Aa31sc209G100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2273' => 'aag', 'Actinidia08896' => 'ach', 'Actinidia10799' => 'ach', 'Actinidia12727' => 'ach', 'Actinidia25377' => 'ach', 'Actinidia32922' => 'ach', 'Actinidia32923' => 'ach', 'Actinidia33442' => 'ach', 'Actinidia36833' => 'ach', 'Actinidia38291' => 'ach', 'Ah.02g114680' => 'amhyb', 'Ah.05g176080' => 'amhyb', 'Ah.11g041900' => 'amhyb', 'Ah.11g046540' => 'amhyb', 'AL1G10490' => 'aly', 'AL3G43340' => 'aly', 'AL4G44910' => 'aly', 'AL8G25090' => 'aly', 'Aqoxy1G04183' => 'aox', 'Aqoxy3G01748' => 'aox', 'Aqoxy7G00446' => 'aox', 'Aqoxy7G01109' => 'aox', 'arahy.Tifrunner.gnm1.ann1.831W35' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S1D52P' => 'arhy', 'AT1G01830' => 'ath', 'AT2G05810' => 'ath', 'AT2G45720' => 'ath', 'AT5G50900' => 'ath', 'ATR0178G015' => 'atr', 'ATR0582G114' => 'atr', 'ATR0757G140' => 'atr', 'Atru.chr5.408' => 'acertr', 'Atru.chr6.1892' => 'acertr', 'Atru.chr6.3257' => 'acertr', 'Atru.chr6.3258' => 'acertr', 'AUR62022741' => 'cqu', 'AUR62029532' => 'cqu', 'AUR62034787' => 'cqu', 'BcaB01g03256' => 'bca', 'BcaB02g09017' => 'bca', 'BcaB03g13618' => 'bca', 'BcaB03g13620' => 'bca', 'BcaB03g13621' => 'bca', 'BcaB05g24024' => 'bca', 'BcaC01g05109' => 'bca', 'BcaC01g06057' => 'bca', 'BcaC02g12191' => 'bca', 'BcaC03g14631' => 'bca', 'BcaC05g25107' => 'bca', 'BcaC05g27296' => 'bca', 'BolC2t08206H' => 'bol', 'BolC3t14326H' => 'bol', 'BolC3t15373H' => 'bol', 'BolC4t22285H' => 'bol', 'BolC4t27180H' => 'bol', 'BolC5t28813H' => 'bol', 'BolC5t34563H' => 'bol', 'BolC6t39515H' => 'bol', 'BraA02t06316Z' => 'bra', 'BraA03t10939Z' => 'bra', 'BraA03t11739Z' => 'bra', 'BraA05t19538Z' => 'bra', 'BraA06t25034Z' => 'bra', 'BraA10t42300Z' => 'bra', 'C02p20640' => 'bna', 'C03p19450' => 'bna', 'C03p30230' => 'bna', 'C03p30240' => 'bna', 'C04p06630' => 'bna', 'C04p56540' => 'bna', 'C05p00240' => 'bna', 'CAN.G170.48' => 'can', 'CAN.G637.60' => 'can', 'CAN.G668.12' => 'can', 'CAN.G735.1' => 'can', 'CANSAT56G1460' => 'cansat', 'CANSAT64G2058' => 'cansat', 'CARHR000500' => 'chi', 'CARHR103390' => 'chi', 'CARHR140960' => 'chi', 'CARHR257360' => 'chi', 'Carub.0001s0038' => 'cru', 'Carub.0003s2704' => 'cru', 'Carub.0004s2838' => 'cru', 'Carub.0008s1090' => 'cru', 'Ca_07863_v3' => 'car', 'Ca_16078_v3' => 'car', 'Ca_23764_v3' => 'car', 'Cc02_g37270' => 'ccan', 'Cc04_g09470' => 'ccan', 'Cc05_g02940' => 'ccan', 'CDE02G1166' => 'cde', 'CDE04G1606' => 'cde', 'CDE04G2305' => 'cde', 'CDE05G1128' => 'cde', 'CDE05G1548' => 'cde', 'CDE05G2390' => 'cde', 'CDE07G0722' => 'cde', 'CDE11G0907' => 'cde', 'Cfa001848' => 'cfa', 'Cfa014318' => 'cfa', 'Cfa018730' => 'cfa', 'Cfa019182' => 'cfa', 'Ciclev10014736m.g' => 'ccl', 'Ciclev10019530m.g' => 'ccl', 'Ciclev10031112m.g' => 'ccl', 'CiPaw.01G054100' => 'cil', 'CiPaw.02G025000' => 'cil', 'CiPaw.03G155100' => 'cil', 'CiPaw.12G001800' => 'cil', 'ClCG01G009870' => 'cla', 'ClCG06G000080' => 'cla', 'ClCG09G011210' => 'cla', 'COL.COLO4_12620' => 'col', 'COL.COLO4_16683' => 'col', 'COL.COLO4_21880' => 'col', 'Cpa.g.sc132.23' => 'cpa', 'Cpa.g.sc18.193' => 'cpa', 'Cpa.g.sc4.117' => 'cpa', 'CsaV3_1G045910' => 'csa', 'CsaV3_3G009280' => 'csa', 'CsaV3_6G005820' => 'csa', 'CsaV3_6G037750' => 'csa', 'CSS0001436' => 'camsi', 'CSS0006224' => 'camsi', 'CSS0007451' => 'camsi', 'CSS0026727' => 'camsi', 'CSS0027248' => 'camsi', 'DCAR_006908' => 'dca', 'DCAR_008589' => 'dca', 'DCAR_016005' => 'dca', 'DCAR_016359' => 'dca', 'DCAR_021139' => 'dca', 'DCAR_025168' => 'dca', 'Dinv01682' => 'din', 'Dinv02290' => 'din', 'Dinv07688' => 'din', 'Dinv08717' => 'din', 'Dinv08718' => 'din', 'Dinv11215' => 'din', 'Dinv23197' => 'din', 'Dinv32426' => 'din', 'Dinv43760' => 'din', 'Duzib084G0402' => 'dzi', 'Duzib133G0533' => 'dzi', 'Duzib133G1567' => 'dzi', 'Duzib138G0129' => 'dzi', 'Duzib138G0708' => 'dzi', 'Duzib205G0014' => 'dzi', 'ECA232G2864' => 'eca', 'ECA234G1829' => 'eca', 'ECA236G2381' => 'eca', 'ECA240G4808' => 'eca', 'ECA247G0908' => 'eca', 'EL10Ac1g00981' => 'bvu', 'EL10Ac5g11336' => 'bvu', 'Eucgr.D02240' => 'egr', 'Eucgr.E00215' => 'egr', 'Eucgr.K00753' => 'egr', 'Eucgr.K02202' => 'egr', 'FAN01G2298' => 'fan', 'FAN02G0691' => 'fan', 'FAN03G2727' => 'fan', 'FAN04G0867' => 'fan', 'FAN05G2749' => 'fan', 'FAN06G3807' => 'fan', 'FAN06G3943' => 'fan', 'FAN08G3029' => 'fan', 'FAN10G0565' => 'fan', 'FAN10G3637' => 'fan', 'FAN11G2541' => 'fan', 'FAN13G1444' => 'fan', 'FAN14G2477' => 'fan', 'FAN18G4028' => 'fan', 'FAN20G2098' => 'fan', 'FvH4_1g21781' => 'fve', 'FvH4_3g23060' => 'fve', 'FvH4_5g09100' => 'fve', 'FvH4_6g42120' => 'fve', 'FvH4_7g13170' => 'fve', 'Glyma.03G017100' => 'gma', 'Glyma.04G199500' => 'gma', 'Glyma.06G166000' => 'gma', 'Glyma.07G078200' => 'gma', 'Glyma.09G264600' => 'gma', 'Glyma.18G227400' => 'gma', 'Gohir.A07G047900' => 'ghi', 'Gohir.A09G247700' => 'ghi', 'Gohir.A11G085100' => 'ghi', 'Gohir.A11G152900' => 'ghi', 'Gohir.A12G103900' => 'ghi', 'Gohir.D07G052200' => 'ghi', 'Gohir.D07G193900' => 'ghi', 'Gohir.D08G150800' => 'ghi', 'Gohir.D09G248500' => 'ghi', 'Gohir.D11G089200' => 'ghi', 'Gohir.D11G159700' => 'ghi', 'Gohir.D12G107350' => 'ghi', 'Gorai.001G055200' => 'gra', 'Gorai.001G217000' => 'gra', 'Gorai.004G156500' => 'gra', 'Gorai.006G272800' => 'gra', 'Gorai.007G095200' => 'gra', 'Gorai.007G170300' => 'gra', 'Gorai.008G116900' => 'gra', 'GSVIVG01008619001' => 'vvi', 'GSVIVG01027519001' => 'vvi', 'GSVIVG01030505001' => 'vvi', 'HanXRQChr02g0059861' => 'han', 'HanXRQChr03g0093551' => 'han', 'HanXRQChr04g0121801' => 'han', 'HanXRQChr09g0273601' => 'han', 'HanXRQChr10g0305911' => 'han', 'HanXRQChr12g0379771' => 'han', 'Haze_07122' => 'cav', 'Haze_12766' => 'cav', 'Haze_15221' => 'cav', 'Hma1.2p1_0046F.1_g027600' => 'hma', 'Hma1.2p1_0168F.1_g074170' => 'hma', 'Hma1.2p1_0177F.1_g078080' => 'hma', 'Hma1.2p1_0398F.1_g143880' => 'hma', 'Hma1.2p1_0507F.1_g168650' => 'hma', 'HPP92_015046' => 'vpl', 'HPP92_020101' => 'vpl', 'HPP92_021878' => 'vpl', 'HPP92_022031' => 'vpl', 'Hund27323' => 'sun', 'Lalb_Chr10g0097491' => 'lal', 'Lalb_Chr11g0069311' => 'lal', 'Lalb_Chr19g0127111' => 'lal', 'Lalb_Chr23g0272951' => 'lal', 'Lj1g0001437' => 'lja', 'Lj1g0009283' => 'lja', 'Lj3g0011074' => 'lja', 'Lj5C91T4' => 'lonja', 'Lj7C519T6' => 'lonja', 'Lj8E130T2' => 'lonja', 'Lj9A484T65' => 'lonja', 'Lj9E577T0' => 'lonja', 'Lj9P577T25' => 'lonja', 'Lsat_1_v5_gn_1_32360' => 'lsa', 'Lsat_1_v5_gn_3_135740' => 'lsa', 'Lsat_1_v5_gn_4_84081' => 'lsa', 'Lsat_1_v5_gn_5_124581' => 'lsa', 'Lsat_1_v5_gn_7_5921' => 'lsa', 'Lsat_1_v5_gn_9_105840' => 'lsa', 'Manes.01G262000' => 'mes', 'Manes.05G039900' => 'mes', 'Manes.06G124800' => 'mes', 'Manes.12G069600' => 'mes', 'Manes.14G046700' => 'mes', 'Mapoly0059s0060' => 'mpo', 'MBI04_g35780_MAGBIO' => 'mbi', 'MBI11_g14284_MAGBIO' => 'mbi', 'MBI12_g31186_MAGBIO' => 'mbi', 'MBI15_g10495_MAGBIO' => 'mbi', 'MBI15_g33086_MAGBIO' => 'mbi', 'MBI16_g26183_MAGBIO' => 'mbi', 'MD01G1051300' => 'mdo', 'MD06G1133700' => 'mdo', 'MD09G1114400' => 'mdo', 'MD14G1150000' => 'mdo', 'MD17G1106100' => 'mdo', 'Medtr3g098730' => 'mtr', 'Medtr5g092900' => 'mtr', 'Medtr7g076220' => 'mtr', 'Medtr8g032570' => 'mtr', 'MELO3C002901.2' => 'cme', 'MELO3C006148.2' => 'cme', 'MELO3C014434.2' => 'cme', 'MELO3C021709.2' => 'cme', 'MELO3C022530.2' => 'cme', 'MELO3C033774.2' => 'cme', 'MELO3C035651.2' => 'cme', 'Migut.B01692' => 'egut', 'Migut.H01239' => 'egut', 'Migut.M00424' => 'egut', 'Migut.O00351' => 'egut', 'MSTRG.11257' => 'ama', 'MSTRG.14135' => 'ama', 'MSTRG.14860' => 'ama', 'MSTRG.20795' => 'ama', 'MSTRG.4626' => 'ama', 'Nitab4.5_0000482g0290' => 'nta', 'Nitab4.5_0001451g0010' => 'nta', 'Nitab4.5_0001825g0010' => 'nta', 'Nitab4.5_0002718g0010' => 'nta', 'Nitab4.5_0004550g0060' => 'nta', 'Nitab4.5_0005008g0030' => 'nta', 'Nn1g01358' => 'nnu', 'Nn2g10462' => 'nnu', 'Nn3g16332' => 'nnu', 'Oeu003101.1' => 'oeu', 'Oeu017976.1' => 'oeu', 'Oeu019019.1' => 'oeu', 'Oeu024410.1' => 'oeu', 'Oeu024412.1' => 'oeu', 'Oeu025068.2' => 'oeu', 'Oeu058113.1' => 'oeu', 'Oeu058606.2' => 'oeu', 'Oeu059233.1' => 'oeu', 'Os03g0116900' => 'osa', 'Os09g0135800' => 'osa', 'Os10g0522601' => 'osa', 'Os11g0515000' => 'osa', 'Peaxi162Scf00021g00064' => 'pax', 'Peaxi162Scf00171g00113' => 'pax', 'Peaxi162Scf00921g00217' => 'pax', 'PGR031G0682' => 'pgr', 'PGR042G2831' => 'pgr', 'PGR044G0706' => 'pgr', 'PGR142G3726' => 'pgr', 'PGSC0003DMG400000663' => 'stu', 'PGSC0003DMG400002873' => 'stu', 'PGSC0003DMG400012021' => 'stu', 'PGSC0003DMG400027764' => 'stu', 'Phvul.008G071700' => 'pvu', 'Phvul.009G163700' => 'pvu', 'Phvul.010G092100' => 'pvu', 'Potri.002G153700' => 'ptr', 'Potri.002G224400' => 'ptr', 'Potri.012G104400' => 'ptr', 'Potri.014G076500' => 'ptr', 'Potri.014G158700' => 'ptr', 'Potri.015G103700' => 'ptr', 'Pp3c14_6300' => 'ppa', 'Pp3c17_11760' => 'ppa', 'Pp3c17_11764' => 'ppa', 'Pp3c1_27190' => 'ppa', 'Pp3c2_15540' => 'ppa', 'Prupe.2G155000' => 'ppe', 'Prupe.3G210100' => 'ppe', 'Prupe.5G144800' => 'ppe', 'Psat3g113240' => 'psa', 'Psat4g199280' => 'psa', 'Psat5g053840' => 'psa', 'PSO017G0138' => 'pso', 'PSO478G0337' => 'pso', 'PSO478G2570' => 'pso', 'PSO478G3591' => 'pso', 'PSO782G2974' => 'pso', 'PSO782G5226' => 'pso', 'QL08p030667' => 'qlo', 'QL08p050579' => 'qlo', 'QL10p001085' => 'qlo', 'RcHm_v2.0_Chr1g0352331' => 'rch', 'RcHm_v2.0_Chr2g0158031' => 'rch', 'RcHm_v2.0_Chr7g0189111' => 'rch', 'RcHm_v2.0_Chr7g0211441' => 'rch', 'Rhsim01G0154600' => 'rsi', 'Rhsim04G0050300' => 'rsi', 'Rhsim07G0020800' => 'rsi', 'Rhsim12G0178700' => 'rsi', 'Sabra02G0121800' => 'sbr', 'Sabra12G0076800' => 'sbr', 'Sabra14G0055700' => 'sbr', 'Sabra14G0120500' => 'sbr', 'Sabra15G0123200' => 'sbr', 'SalBow1G7783' => 'sbo', 'SalBow1G8237' => 'sbo', 'SalBow3G2146' => 'sbo', 'SalBow4G1272' => 'sbo', 'SalBow4G2769' => 'sbo', 'SalBow5G4207' => 'sbo', 'SalBow5G4223' => 'sbo', 'SalBow6G1927' => 'sbo', 'SalBow7G4227' => 'sbo', 'SalBow8G5045' => 'sbo', 'Sc02g0002200' => 'sci', 'Sc04g0000320' => 'sci', 'Sc06g0009660' => 'sci', 'Sc23g0003260' => 'sci', 'Sed0000393' => 'sed', 'Sed0003645' => 'sed', 'Sed0003646' => 'sed', 'Sed0004904' => 'sed', 'Sed0009631' => 'sed', 'Sed0013255' => 'sed', 'Sed0022908' => 'sed', 'SEGI_04334' => 'sgi', 'SEGI_14099' => 'sgi', 'SEGI_15798' => 'sgi', 'SEGI_41007' => 'sgi', 'SGA_v2.0_scaffold142G35695' => 'sas', 'SGA_v2.0_scaffold153G37070' => 'sas', 'SGA_v2.0_scaffold159G37557' => 'sas', 'SGA_v2.0_scaffold34G13759' => 'sas', 'SGA_v2.0_scaffold40G15596' => 'sas', 'SGA_v2.0_scaffold47G17576' => 'sas', 'SGA_v2.0_scaffold540G52804' => 'sas', 'SGA_v2.0_scaffold540G52808' => 'sas', 'SGA_v2.0_scaffold70G23388' => 'sas', 'SHI14133' => 'shi', 'SMO347G0222' => 'smo', 'SMO347G0609' => 'smo', 'Solyc01g091740.4' => 'sly', 'Solyc03g097740.1' => 'sly', 'Solyc07g049390.3' => 'sly', 'Sopen01g037520' => 'spe', 'Sopen03g028480' => 'spe', 'Sopen07g024730' => 'spe', 'Sp1g00450' => 'spa', 'Sp4g27770' => 'spa', 'Sp6g13030' => 'spa', 'TAR020G0002' => 'tar', 'TAR371G0001' => 'tar', 'TAR374G1300' => 'tar', 'TAR375G0524' => 'tar', 'TAR629G0250' => 'tar', 'TAR629G2076' => 'tar', 'TAR629G3251' => 'tar', 'TAR636G0933' => 'tar', 'THA.LOC104802011' => 'tha', 'THA.LOC104808043' => 'tha', 'THA.LOC104809646' => 'tha', 'THA.LOC104814093' => 'tha', 'Thecc.01G182300' => 'tca', 'Thecc.01G368200' => 'tca', 'Thecc.03G137400' => 'tca', 'Thhalv10001387m.g' => 'esa', 'Thhalv10007207m.g' => 'esa', 'Thhalv10013161m.g' => 'esa', 'Thhalv10028711m.g' => 'esa', 'TPR.G17602' => 'tpr', 'TPR.G21579' => 'tpr', 'TPR.G37857' => 'tpr', 'TWI14G0610' => 'twi', 'TWI23G0437' => 'twi', 'TWI23G0836' => 'twi', 'TWI36G0748' => 'twi', 'TWI39G1035' => 'twi', 'TWI59G0102' => 'twi', 'unitig_0.g1285' => 'ugi', 'unitig_22.g5364' => 'ugi', 'unitig_26.g9927' => 'ugi', 'unitig_27.g25085' => 'ugi', 'unitig_27.g25086' => 'ugi', 'unitig_52.g17332' => 'ugi', 'unitig_61.g26401' => 'ugi', 'unitig_744.g24640' => 'ugi', 'vmacro13335' => 'vma', 'vmacro20969' => 'vma', 'VMungo0331G1950' => 'vmu', 'VMungo1309G2808' => 'vmu', 'VMungo1309G3027' => 'vmu', 'VMungo1383G0510' => 'vmu', 'Zm00001eb001150' => 'zma', 'Zm00001eb021400' => 'zma', 'Zm00001eb095530' => 'zma', 'Zm00001eb113050' => 'zma', 'Zm00001eb170220' => 'zma' ) $gf_id = 'HOM05D001356' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001356' ) $data_identifier = 'HOM05D001356' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 7, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 5, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 10, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 9, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb170220' $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